David M. Kristensen
David M. Kristensen
University of Iowa, Department of Biomedical Engineering
Verified email at uiowa.edu
Cited by
Cited by
New dimensions of the virus world discovered through metagenomics
DM Kristensen, AR Mushegian, VV Dolja, EV Koonin
Trends in microbiology 18 (1), 11-19, 2010
Structural clusters of evolutionary trace residues are statistically significant and common in proteins
S Madabushi, H Yao, M Marsh, DM Kristensen, A Philippi, ME Sowa, ...
Journal of molecular biology 316 (1), 139-154, 2002
An accurate, sensitive, and scalable method to identify functional sites in protein structures
H Yao, DM Kristensen, I Mihalek, ME Sowa, C Shaw, M Kimmel, L Kavraki, ...
Journal of molecular biology 326 (1), 255-261, 2003
Computational methods for Gene Orthology inference
DM Kristensen, YI Wolf, AR Mushegian, EV Koonin
Briefings in bioinformatics 12 (5), 379-391, 2011
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches
DM Kristensen, L Kannan, MK Coleman, YI Wolf, A Sorokin, EV Koonin, ...
Bioinformatics 26 (12), 1481-1487, 2010
Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation
AL Grazziotin, EV Koonin, DM Kristensen
Nucleic acids research, gkw975, 2016
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
P Puigb˛, AE Lobkovsky, DM Kristensen, YI Wolf, EV Koonin
BMC biology 12 (1), 66, 2014
Ligand-free and-bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of theá…
S Trakhanov, NK Vyas, H Luecke, DM Kristensen, J Ma, FA Quiocho
Biochemistry 44 (17), 6597-6608, 2005
Classification and quantification of bacteriophage taxa in human gut metagenomes
AS Waller, T Yamada, DM Kristensen, JR Kultima, S Sunagawa, ...
The ISME journal 8 (7), 1391-1402, 2014
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes
DM Kristensen, AS Waller, T Yamada, P Bork, AR Mushegian, EV Koonin
Journal of bacteriology 195 (5), 941-950, 2013
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
DM Kristensen, RM Ward, AM Lisewski, S Erdin, BY Chen, VY Fofanov, ...
BMC bioinformatics 9 (1), 1-19, 2008
ET viewer: an application for predicting and visualizing functional sites in protein structures
DH Morgan, DM Kristensen, D Mittelman, O Lichtarge
Bioinformatics 22 (16), 2049-2050, 2006
No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales
U Gophna, DM Kristensen, YI Wolf, O Popa, C Drevet, EV Koonin
The ISME journal 9 (9), 2021-2027, 2015
Accurate and scalable identification of functional sites by evolutionary tracing
O Lichtarge, H Yao, DM Kristensen, S Madabushi, I Mihalek
Journal of structural and functional genomics 4 (2-3), 159-166, 2003
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs
BY Chen, VY Fofanov, DH Bryant, BD Dodson, DM Kristensen, ...
Journal of Computational Biology 14 (6), 791-816, 2007
Algorithms for structural comparison and statistical analysis of 3D protein motifs
BY Chen, VY Fofanov, DM Kristensen, M Kimmel, O Lichtarge, LE Kavraki
Biocomputing 2005, 334-345, 2005
Contribution of phage‐derived genomic islands to the virulence of facultative bacterial pathogens
B Busby, DM Kristensen, EV Koonin
Environmental microbiology 15 (2), 307-312, 2013
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
R Matthew Ward, E Venner, B Daines, S Murray, S Erdin, DM Kristensen, ...
Bioinformatics 25 (11), 1426-1427, 2009
Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts
DM Kristensen, X Cai, A Mushegian
Journal of bacteriology 193 (8), 1806-1814, 2011
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity
DM Kristensen, BY Chen, VY Fofanov, RM Ward, AM Lisewski, M Kimmel, ...
Protein Science 15 (6), 1530-1536, 2006
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